The aim of the present study was to determine whether p16 gene is involved in the genesis of primary hepatocellular carcinoma (HCC). Twenty-five primary HCC tumor and corresponding non-tumor liver tissue specimens were examined for P16 gene alterations. The identification of deletion of p16 gene exon 1 and exon 2 was performed using comparative multiplex polymerase chain reaction (PCR) analysis. The point mutation of p16 gene exon 2 was investigated by single strand conformational polymorphism(SSCP) analysis, and the status of p16 gene methylation was screened using PCR-based methylation analysis. Moreover, 35 parafin specimens of primary HCCs with corresponding non-tumor liver tissues, including the 25 cases described above for screening of p16 gene alterations, were investigated also for P16 protein expression by using immunohistochemical analysis. The results of comparative multiplex PCR analysis showed that 12% (3/25) p16 gene deletions, including homozygous deletions in 2 tumors and hemizygous deletion in 1 tumor, were found in the primary HCCs samples. No point mutation was identified in the remaining 22 tumor samples without p16 gene deletions by using SSCP analysis. Hypermethylation was detected in 24% (6/25) of tumor samples by PCR-based analysis. However the corresponding non-tumor liver tissue specimens were always unmethylated at p16 locus. Loss of P16 protein expression, detected by immunohistochemistry, occurred in 16 of 35 (45.7%) tumor samples, whereas all the non-tumor liver tissue specimens showed positive p16 staining. These results indicate that inactivation of p16 gene is relevant to the genesis of HCC.